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comparison funannotate_predict.xml @ 0:40b87aef5241 draft

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"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
author iuc
date Thu, 26 Aug 2021 06:55:33 +0000
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children 1a59958c1f76
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1 <tool id="funannotate_predict" name="Funannotate predict annotation" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <expand macro="requirements" />
8 </requirements>
9 <version_command><![CDATA[funannotate check --show-versions]]></version_command>
10 <command><![CDATA[
11 #if $genemark.genemark_license:
12 if [ -z "\$GENEMARK_PATH" ] ; then echo "GeneMark is not installed on this Galaxy server." >&2 ; exit 1 ; fi &&
13 if [ ! -f "\$GENEMARK_PATH/gmes_petap.pl" ] ; then echo "GeneMark is not installed properly on this Galaxy server." >&2 ; exit 1 ; fi &&
14 ## GeneMark only search for license in ~/.gm_key
15 cp '${genemark.genemark_license}' ~/.gm_key &&
16 #end if
17
18 #if $uglyTestingHack == "true":
19 ## funannotate_db contains some hard coded path, need to rewrite one for tests (not in real life when using data manager)
20 ## Need to copy too as the test_data is read only on CI
21 cp -r '${database.fields.path}' './hacked_database' &&
22 sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' &&
23 #end if
24
25 funannotate predict
26 --input '${input}'
27 --out output
28
29 #if $uglyTestingHack == "true":
30 --database `pwd`'/hacked_database'
31 #else
32 --database '$database.fields.path'
33 #end if
34
35 --species '${organism.species}'
36 --isolate '${organism.isolate}'
37 --strain '${organism.strain}'
38 --organism '${organism.organism}'
39 --ploidy ${organism.ploidy}
40 --SeqCenter '${organism.SeqCenter}'
41 --SeqAccession '${organism.SeqAccession}'
42 --name '${organism.name}'
43 --numbering ${organism.numbering}
44
45 #if $parameters:
46 --parameters '${parameters}'
47 #end if
48
49 #if $evidences.rna_bam:
50 --rna_bam ${evidences.rna_bam}
51 #end if
52
53 #set est_list = ""
54 #if len($evidences.transcript_evidence) > 0:
55 #for $estev in $evidences.transcript_evidence:
56 #if $estev:
57 #set est_list += " '" + str($estev) + "'"
58 #end if
59 #end for
60 #end if
61 #if $est_list:
62 --transcript_evidence $est_list
63 #end if
64
65 #if $evidences.prot_evidence == 'custom':
66 --protein_evidence
67 #for $protev in $evidences.protein_evidence:
68 '${protev}'
69 #end for
70 #end if
71 --p2g_pident ${evidences.p2g_pident}
72 --p2g_prefilter ${evidences.p2g_prefilter}
73
74 #if $augustus.augustus_species != 'none':
75 --augustus_species '${augustus.augustus_species}'
76 #end if
77 --min_training_models ${augustus.min_training_models}
78 ${augustus.optimize_augustus}
79
80 #if $genemark.genemark_license:
81 --genemark_mode '${genemark.genemark_mode}'
82 #if $genemark.genemark_mod:
83 --genemark_mod '${genemark.genemark_mod}'
84 #end if
85 --soft_mask ${genemark.soft_mask}
86 #end if
87
88 --busco_seed_species '${busco.busco_seed_species}'
89 --busco_db '${busco.busco_db}'
90
91 $evm.repeats2evm
92 #if $evm.evm_partitioning.evm_partition == "yes":
93 --evm-partition-interval ${evm.evm_partitioning.evm_partition_interval}
94 #else:
95 --no-evm-partitions
96 #end if
97 #if $evm.weights:
98 --weights '${evm.weights}'
99 #end if
100
101 #if $other_predictors.stringtie:
102 --stringtie '${other_predictors.stringtie}'
103 #end if
104 #if $other_predictors.maker_gff:
105 --maker_gff '${other_predictors.maker_gff}'
106 #end if
107 #if $other_predictors.pasa_gff:
108 --pasa_gff '${other_predictors.pasa_gff}:${other_predictors.pasa_gff_weight}'
109 #end if
110 #if $other_predictors.other_gff:
111 --other_gff '${other_predictors.other_gff}:${other_predictors.other_gff_weight}'
112 #end if
113
114 --min_intronlen ${filtering.min_intronlen}
115 --max_intronlen ${filtering.max_intronlen}
116 --min_protlen ${filtering.min_protlen}
117 ${filtering.keep_no_stops}
118 --repeat_filter ${filtering.repeat_filter}
119
120 --cpus \${GALAXY_SLOTS:-2}
121
122 &&
123
124 mv output/predict_results/*.gbk out.gbk &&
125 mv output/predict_results/*.tbl out.tbl &&
126 mv output/predict_results/*.gff3 out.gff3 &&
127 mv output/predict_results/*.proteins.fa out.proteins.fa &&
128 mv output/predict_results/*.mrna-transcripts.fa out.mrna-transcripts.fa &&
129 mv output/predict_results/*.cds-transcripts.fa out.cds-transcripts.fa &&
130 mv output/predict_results/*.discrepency.report.txt out.discrepency.report.txt &&
131 mv output/predict_results/*.error.summary.txt out.error.summary.txt &&
132 mv output/predict_results/*.validation.txt out.validation.txt &&
133 mv output/predict_results/*.stats.json out.stats.json
134 ]]></command>
135 <inputs>
136 <param argument="--input" type="data" format="fasta" label="Assembly to annotate" help="The assembly should be soft-masked (with RepeatMasker for example)" />
137
138 <param name="database" label="Funannotate database" type="select">
139 <options from_data_table="funannotate">
140 <column name="value" index="0" />
141 <column name="name" index="1" />
142 <column name="path" index="3" />
143 <filter type="sort_by" column="0" />
144 <filter type="static_value" column="2" value="1.0" />
145 </options>
146 </param>
147
148 <section name="organism" expanded="true" title="Organism">
149 <param argument="--species" type="text" optional="false" label="Name of the species to annotate" help="e.g. Genus species">
150 <validator type="empty_field" />
151 </param>
152 <param argument="--isolate" type="text" label="Isolate name" help="If relevant (e.g. Af293)" />
153 <param argument="--strain" type="text" label="Strain name" help="If relevant (e.g. FGSCA4)" />
154 <param argument="--organism" type="boolean" checked="false" truevalue="fungus" falsevalue="other" label="Is it a fungus species?" />
155 <param argument="--ploidy" type="integer" value="1" label="Ploidy of assembly" />
156 <param argument="--SeqCenter" type="text" value="CFMR" label="Sequencing facility for NCBI tbl file" />
157 <param argument="--SeqAccession" type="text" value="12345" label="Sequence accession number for NCBI tbl file" />
158 <param argument="--name" type="text" value="FUN_" label="Locus tag prefix" help="Will prefix all the gene names" />
159 <param argument="--numbering" type="integer" value="1" label="Specify where gene numbering starts" />
160 </section>
161
162 <section name="evidences" expanded="true" title="Evidences">
163 <param argument="--rna_bam" type="data" format="bam" optional="true" label="RNA-seq mapped to genome to train Augustus/GeneMark-ET" />
164 <param argument="--transcript_evidence" type="data" format="fasta" multiple="true" optional="true" label="mRNA/ESTs to align to genome" />
165 <conditional name="prot_evidence">
166 <param name="prot_evidence_source" type="select" label="Select protein evidences">
167 <option value="uniprot" selected="True">Use UniProtKb/SwissProt (from selected Funannotate database)</option>
168 <option value="custom">Custom protein sequences</option>
169 </param>
170 <when value="uniprot"/>
171 <when value="custom">
172 <param argument="--protein_evidence" type="data" format="fasta" multiple="true" label="Proteins to map to genome" />
173 </when>
174 </conditional>
175 <param argument="--p2g_pident" type="integer" value="80" label="Exonerate percent identity (for proteins)" />
176 <param argument="--p2g_prefilter" type="select" label="Prefilter hists with (for proteins)">
177 <option value="diamond" selected="True">Diamond</option>
178 <option value="tblastn">tblastn (slower)</option>
179 </param>
180 </section>
181
182 <param argument="--parameters" type="data" format="json" optional="true" label="Ab-initio training parameters from a previous run" help="If specified, will over-rule any other training presets based on sepcies selection." />
183
184 <section name="other_predictors" expanded="false" title="Other annotations">
185 <param argument="--stringtie" type="data" format="gtf" optional="true" label="StringTie GTF result" />
186 <param argument="--maker_gff" type="data" format="gff3" optional="true" label="MAKER2 GFF file" help="Parse results directly to EVM" />
187 <param argument="--pasa_gff" type="data" format="gff3" optional="true" label="PASA generated gene models" />
188 <param name="pasa_gff_weight" type="integer" value="1" label="Weight for PASA generated gene models" />
189 <param argument="--other_gff" type="data" format="gff3" optional="true" label="Annotation pass-through to EVM" />
190 <param name="other_gff_weight" type="integer" value="1" label="Weight for annotation pass-through to EVM" />
191 </section>
192
193 <section name="augustus" expanded="true" title="Augustus settings">
194 <param argument="--augustus_species" type="select" label="Augustus species training set" help="Select a species from the list">
195 <option value="none" selected="True">No corresponding species, train from scratch</option>
196 <expand macro="augustus_species"/>
197 </param>
198 <param argument="--min_training_models" type="integer" value="200" label="Minimum number of models to train Augustus" />
199 <param argument="--optimize_augustus" type="boolean" checked="false" truevalue="--optimize_augustus" falsevalue="" label="Run 'optimize_augustus.pl' to refine training (long runtime)" />
200 </section>
201
202 <section name="genemark" expanded="false" title="GeneMark settings">
203 <param name="genemark_license" type="data" format="txt" optional="true" label="GeneMark license file" help="GeneMark is not a free software, to use it download and unzip a license from http://topaz.gatech.edu/GeneMark/license_download.cgi (ES/ET/EP version). GeneMark needs to be installed manually by Galaxy administrators, it might not be available on this server." />
204 <param argument="--genemark_mode" type="select" label="GeneMark mode">
205 <option value="ES" selected="True">ES</option>
206 <option value="ET">ET</option>
207 </param>
208 <param argument="--genemark_mod" type="data" format="txt" optional="true" label="Use pre-existing Genemark training file (e.g. gmhmm.mod)" />
209 <param argument="--soft_mask" type="integer" value="2000" label="Softmasked length threshold for GeneMark" help="GeneMark will skip prediction on repeat regions shorter than this value" />
210 </section>
211
212 <section name="busco" expanded="true" title="BUSCO settings">
213 <param argument="--busco_seed_species" type="select" label="Initial Augustus species training set for BUSCO alignment" help="Select the closest species. BUSCO will only be used if no RNASeq (bam) data is given as evidence.">
214 <expand macro="augustus_species"/>
215 </param>
216 <param argument="--busco_db" type="select" label="BUSCO models to align" help="BUSCO will only be used if no RNASeq (bam) data is given as evidence.">
217 <expand macro="busco_species"/>
218 </param>
219 </section>
220
221 <section name="evm" expanded="false" title="EVM settings">
222 <param argument="--repeats2evm" type="boolean" checked="false" truevalue="--repeats2evm" falsevalue="" label="Use repeats in EVM consensus model building" help="Not recommended for fungal genomes that have high gene density. You might want to turn this option on for larger genomes or those that have a high repeat content." />
223 <conditional name="evm_partitioning">
224 <param name="evm_partition" type="select" label="Split contigs into partitions for EVM processing?" help="Splits big contigs in smaller overlaping chunks to reduce memory usage and parallelize">
225 <option value="yes" selected="True">Yes</option>
226 <option value="no">No</option>
227 </param>
228 <when value="yes">
229 <param argument="--evm-partition-interval" type="integer" value="1500" label="Min length between genes to make a partition" />
230 </when>
231 <when value="no"/>
232 </conditional>
233 <param argument="--weights" type="text" optional="true" label="Custom ab-initio predictor and EVM weight" help="e.g. augustus:2 pasa:10">
234 <validator type="regex" message="Key must consist of alphanumeric characters only, possibly separated by the period character ('.')">^[\w: ]+$</validator>
235 </param>
236 </section>
237
238 <section name="filtering" expanded="true" title="Filtering">
239 <param argument="--min_intronlen" type="integer" value="10" label="Minimum intron length" />
240 <param argument="--max_intronlen" type="integer" value="3000" label="Maximum intron length" />
241 <param argument="--min_protlen" type="integer" value="50" label="Minimum protein length" />
242 <param argument="--keep_no_stops" type="boolean" checked="false" truevalue="--keep_no_stops" falsevalue="" label="Keep gene models without valid stops" />
243 <param argument="--repeat_filter" type="select" label="Repetitive gene model filtering" help="'overlap' drops gene models that are more than 90% contained within a repeat region; 'blast' compares the amino acid sequences to a small database of known transposons">
244 <option value="overlap blast" selected="True">overlap + blast</option>
245 <option value="overlap">overlap</option>
246 <option value="blast">blast</option>
247 <option value="none">none</option>
248 </param>
249 </section>
250
251 <!-- Need this to change path in the test funannotate_db -->
252 <param type="hidden" name="uglyTestingHack" value="" />
253 </inputs>
254 <outputs>
255 <data name='annot_gbk' format='genbank' label="${tool.name} on ${on_string}: annotation (genbank)" from_work_dir="out.gbk" />
256 <data name='annot_tbl' format='txt' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="out.tbl" />
257 <data name='annot_gff3' format='gff3' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="out.gff3" />
258 <data name='fasta_proteins' format='fasta' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="out.proteins.fa" />
259 <data name='fasta_transcripts_mrna' format='fasta' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="out.mrna-transcripts.fa" />
260 <data name='fasta_transcripts_cds' format='fasta' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="out.cds-transcripts.fa" />
261 <data name='tbl2asn_report' format='txt' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="out.discrepency.report.txt" />
262 <data name='tbl2asn_error' format='txt' label="${tool.name} on ${on_string}: tbl2asn error summary report" from_work_dir="out.error.summary.txt" />
263 <data name='tbl2asn_validation' format='txt' label="${tool.name} on ${on_string}: tbl2asn genome validation report" from_work_dir="out.validation.txt" />
264 <data name='stats' format='json' label="${tool.name} on ${on_string}: stats" from_work_dir="out.stats.json" />
265 <!-- TODO some day: provide trained models as output, reusable as input to other funannotate runs
266 (parameters.json file references files with absolute paths, would probably need to create an archive + edit paths in parameters.json) -->
267 <!--data name='abinitio' format='json' label="${tool.name} on ${on_string}: ab-initio training parameters" from_work_dir="output/predict_results/*.parameters.json" /-->
268 </outputs>
269 <tests>
270 <!-- training from scratch -->
271 <test>
272 <param name="input" value="genome_masked.fa" />
273 <param name="database" value="2021-07-20-120000" />
274 <section name="organism">
275 <param name="species" value="Genus species" />
276 </section>
277 <section name="augustus">
278 <param name="min_training_models" value="3" />
279 </section>
280 <section name="busco">
281 <param name="busco_seed_species" value="fly" />
282 <param name="busco_db" value="insecta" />
283 </section>
284 <!-- non deterministic results, so can't be more precise here -->
285 <output name="annot_gbk">
286 <assert_contents>
287 <has_text text=" TITLE Direct Submission" />
288 <has_text text="/locus_tag=&quot;FUN_000001&quot;" />
289 </assert_contents>
290 </output>
291 <output name="annot_tbl">
292 <assert_contents>
293 <has_text text=">Feature sample" />
294 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" />
295 </assert_contents>
296 </output>
297 <output name="annot_gff3">
298 <assert_contents>
299 <has_text text="##gff-version 3" />
300 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" />
301 </assert_contents>
302 </output>
303 <output name="fasta_proteins">
304 <assert_contents>
305 <has_text text=">FUN_000001-T1 FUN_000001" />
306 </assert_contents>
307 </output>
308 <output name="fasta_transcripts_mrna">
309 <assert_contents>
310 <has_text text=">FUN_000001-T1 FUN_000001" />
311 </assert_contents>
312 </output>
313 <output name="fasta_transcripts_cds">
314 <assert_contents>
315 <has_text text=">FUN_000001-T1 FUN_000001" />
316 </assert_contents>
317 </output>
318 <!--output name="abinitio" file="predict_scratch/fly.parameters.json" compare="sim_size" /-->
319 <output name="tbl2asn_report" file="predict_scratch/Genus_species.discrepency.report.txt" compare="sim_size" />
320 <output name="tbl2asn_error" file="predict_scratch/Genus_species.error.summary.txt" compare="sim_size" delta="500" />
321 <output name="tbl2asn_validation" file="predict_scratch/Genus_species.validation.txt" compare="sim_size" delta="500" />
322 <output name="stats" file="predict_scratch/Genus_species.stats.json" compare="sim_size" />
323 <assert_stderr>
324 <has_text text="augustus busco"/>
325 <has_text text="glimmerhmm busco"/>
326 <has_text text="snap busco"/>
327 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/>
328 <has_text text="Skipping CodingQuarry as no --rna_bam passed"/>
329 <has_text text="Running Augustus gene prediction using genus_species parameters"/>
330 <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
331 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
332 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
333 <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
334 <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>
335 </assert_stderr>
336 </test>
337
338 <!-- pre-trained augustus -->
339 <test>
340 <param name="input" value="genome_masked.fa" />
341 <param name="database" value="2021-07-20-120000" />
342 <section name="organism">
343 <param name="species" value="Genus species" />
344 </section>
345 <section name="augustus">
346 <param name="augustus_species" value="fly" />
347 </section>
348 <section name="busco">
349 <param name="busco_seed_species" value="fly" />
350 <param name="busco_db" value="insecta" />
351 </section>
352 <param name="uglyTestingHack" value="true" />
353 <!-- non deterministic results, so can't be more precise here -->
354 <output name="annot_gbk">
355 <assert_contents>
356 <has_text text=" TITLE Direct Submission" />
357 <has_text text="/locus_tag=&quot;FUN_000001&quot;" />
358 </assert_contents>
359 </output>
360 <output name="annot_tbl">
361 <assert_contents>
362 <has_text text=">Feature sample" />
363 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" />
364 </assert_contents>
365 </output>
366 <output name="annot_gff3">
367 <assert_contents>
368 <has_text text="##gff-version 3" />
369 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" />
370 </assert_contents>
371 </output>
372 <output name="fasta_proteins">
373 <assert_contents>
374 <has_text text=">FUN_000001-T1 FUN_000001" />
375 </assert_contents>
376 </output>
377 <output name="fasta_transcripts_mrna">
378 <assert_contents>
379 <has_text text=">FUN_000001-T1 FUN_000001" />
380 </assert_contents>
381 </output>
382 <output name="fasta_transcripts_cds">
383 <assert_contents>
384 <has_text text=">FUN_000001-T1 FUN_000001" />
385 </assert_contents>
386 </output>
387 <assert_stderr>
388 <has_text text="augustus pretrained"/>
389 <has_text text="glimmerhmm busco"/>
390 <has_text text="snap busco"/>
391 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/>
392 <has_text text="Skipping CodingQuarry as no --rna_bam passed"/>
393 <has_text text="Running Augustus gene prediction using fly parameters"/>
394 <not_has_text text="Aligning transcript evidence to genome with minimap2"/>
395 <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
396 <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
397 <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
398 <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>
399 </assert_stderr>
400 </test>
401
402 <!-- bam -->
403 <test>
404 <param name="input" value="genome_masked.fa" />
405 <param name="database" value="2021-07-20-120000" />
406 <section name="organism">
407 <param name="species" value="Genus species" />
408 </section>
409 <section name="evidences">
410 <param name="rna_bam" value="SRR7458692.bam" />
411 <param name="transcript_evidence" value="predict_scratch/Genus_species.mrna-transcripts.fa" />
412 <conditional name="prot_evidence">
413 <param name="prot_evidence_source" value="custom" />
414 <param name="protein_evidence" value="predict_scratch/Genus_species.proteins.fa" />
415 </conditional>
416 </section>
417 <section name="augustus">
418 <param name="min_training_models" value="3" />
419 </section>
420 <section name="busco">
421 <param name="busco_seed_species" value="fly" />
422 <param name="busco_db" value="insecta" />
423 </section>
424 <!-- non deterministic results, so can't be more precise here -->
425 <output name="annot_gbk">
426 <assert_contents>
427 <has_text text=" TITLE Direct Submission" />
428 <has_text text="/locus_tag=&quot;FUN_000001&quot;" />
429 </assert_contents>
430 </output>
431 <output name="annot_tbl">
432 <assert_contents>
433 <has_text text=">Feature sample" />
434 <has_text text="gnl|ncbi|FUN_000001-T1_mrna" />
435 </assert_contents>
436 </output>
437 <output name="annot_gff3">
438 <assert_contents>
439 <has_text text="##gff-version 3" />
440 <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" />
441 </assert_contents>
442 </output>
443 <output name="fasta_proteins">
444 <assert_contents>
445 <has_text text=">FUN_000001-T1 FUN_000001" />
446 </assert_contents>
447 </output>
448 <output name="fasta_transcripts_mrna">
449 <assert_contents>
450 <has_text text=">FUN_000001-T1 FUN_000001" />
451 </assert_contents>
452 </output>
453 <output name="fasta_transcripts_cds">
454 <assert_contents>
455 <has_text text=">FUN_000001-T1 FUN_000001" />
456 </assert_contents>
457 </output>
458 <assert_stderr>
459 <has_text text="augustus busco"/>
460 <has_text text="glimmerhmm busco"/>
461 <has_text text="snap busco"/>
462 <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/>
463 <not_has_text text="Skipping CodingQuarry as no --rna_bam passed"/>
464 <has_text text="Running Augustus gene prediction using genus_species parameters"/>
465 <has_text text="Training Augustus using BUSCO gene models"/>
466 <has_text text="Aligning transcript evidence to genome with minimap2"/>
467 <has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>
468 <has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>
469 <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>
470 <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>
471 </assert_stderr>
472 </test>
473 </tests>
474 <help><![CDATA[
475 Funannotate_ predict
476 --------------------
477
478 Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
479
480 Script takes genome multi-fasta file and a variety of inputs to do a comprehensive whole
481 genome gene prediction. Uses AUGUSTUS, GeneMark, Snap, GlimmerHMM, BUSCO, EVidence Modeler,
482 tbl2asn, tRNAScan-SE, Exonerate, minimap2.
483
484 .. _Funannotate: http://funannotate.readthedocs.io
485 ]]></help>
486 <expand macro="citations" />
487 </tool>